The management of wastewater is the fifth largest single source of CH4 emissions and the sixth of N2O. Options to improve sanitation within the Morelos State in Mexico were compared applying a modification of the IPCC guidelines to estimate greenhouse gas (GHG) emissions. A 2030 business-as-usual scenario which considers current sanitation practices and 2010 baseline-scenario, showed that septic tanks, the main state option for sanitation, were the principal source of emissions, even higher than from non-controlled wastewater discharges. These scenarios also revealed that the two metropolitan areas were key in terms of mitigation as they contributed 88% of the total GHG emissions. For the 2030A scenario (sanitation + adaptation), it was seen that if the policy of septic tank usage continues, and the existing wastewater treatment plants are rehabilitated, the GHG emissions would be reduced by 2% compared to the BAU scenario. In contrast, if a policy were adopted considering in addition mitigation measures, 26% GHG emissions reduction might be achieved. Additional co-benefits will be obtained in several sectors, including health (diarrheal and dengue diseases control), agriculture, and the environment, performing a more efficient and integrated management of water and achieving savings on the operating costs of WWTP through co-generation.